Job ID = 6453279 SRX = SRX110790 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:23:47 prefetch.2.10.7: 1) Downloading 'SRR388372'... 2020-06-21T08:23:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:30:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:30:22 prefetch.2.10.7: 1) 'SRR388372' was downloaded successfully Read 30079129 spots for SRR388372/SRR388372.sra Written 30079129 spots for SRR388372/SRR388372.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:41 30079129 reads; of these: 30079129 (100.00%) were unpaired; of these: 2353110 (7.82%) aligned 0 times 23359731 (77.66%) aligned exactly 1 time 4366288 (14.52%) aligned >1 times 92.18% overall alignment rate Time searching: 00:05:41 Overall time: 00:05:41 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 4007734 / 27726019 = 0.1445 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 17:43:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110790/SRX110790.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110790/SRX110790.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110790/SRX110790.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110790/SRX110790.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 17:43:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:43:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:43:49: 1000000 INFO @ Sun, 21 Jun 2020 17:43:55: 2000000 INFO @ Sun, 21 Jun 2020 17:44:00: 3000000 INFO @ Sun, 21 Jun 2020 17:44:06: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 17:44:12: 5000000 INFO @ Sun, 21 Jun 2020 17:44:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110790/SRX110790.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110790/SRX110790.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110790/SRX110790.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110790/SRX110790.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 17:44:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:44:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:44:17: 6000000 INFO @ Sun, 21 Jun 2020 17:44:20: 1000000 INFO @ Sun, 21 Jun 2020 17:44:24: 7000000 INFO @ Sun, 21 Jun 2020 17:44:26: 2000000 INFO @ Sun, 21 Jun 2020 17:44:30: 8000000 INFO @ Sun, 21 Jun 2020 17:44:32: 3000000 INFO @ Sun, 21 Jun 2020 17:44:36: 9000000 INFO @ Sun, 21 Jun 2020 17:44:39: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 17:44:42: 10000000 INFO @ Sun, 21 Jun 2020 17:44:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110790/SRX110790.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110790/SRX110790.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110790/SRX110790.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110790/SRX110790.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 17:44:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:44:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:44:45: 5000000 INFO @ Sun, 21 Jun 2020 17:44:48: 11000000 INFO @ Sun, 21 Jun 2020 17:44:49: 1000000 INFO @ Sun, 21 Jun 2020 17:44:51: 6000000 INFO @ Sun, 21 Jun 2020 17:44:53: 12000000 INFO @ Sun, 21 Jun 2020 17:44:55: 2000000 INFO @ Sun, 21 Jun 2020 17:44:58: 7000000 INFO @ Sun, 21 Jun 2020 17:44:59: 13000000 INFO @ Sun, 21 Jun 2020 17:45:01: 3000000 INFO @ Sun, 21 Jun 2020 17:45:04: 8000000 INFO @ Sun, 21 Jun 2020 17:45:05: 14000000 INFO @ Sun, 21 Jun 2020 17:45:07: 4000000 INFO @ Sun, 21 Jun 2020 17:45:11: 9000000 INFO @ Sun, 21 Jun 2020 17:45:11: 15000000 INFO @ Sun, 21 Jun 2020 17:45:13: 5000000 INFO @ Sun, 21 Jun 2020 17:45:17: 16000000 INFO @ Sun, 21 Jun 2020 17:45:17: 10000000 INFO @ Sun, 21 Jun 2020 17:45:19: 6000000 INFO @ Sun, 21 Jun 2020 17:45:23: 17000000 INFO @ Sun, 21 Jun 2020 17:45:24: 11000000 INFO @ Sun, 21 Jun 2020 17:45:24: 7000000 INFO @ Sun, 21 Jun 2020 17:45:29: 18000000 INFO @ Sun, 21 Jun 2020 17:45:30: 8000000 INFO @ Sun, 21 Jun 2020 17:45:30: 12000000 INFO @ Sun, 21 Jun 2020 17:45:34: 19000000 INFO @ Sun, 21 Jun 2020 17:45:36: 9000000 INFO @ Sun, 21 Jun 2020 17:45:37: 13000000 INFO @ Sun, 21 Jun 2020 17:45:41: 20000000 INFO @ Sun, 21 Jun 2020 17:45:41: 10000000 INFO @ Sun, 21 Jun 2020 17:45:43: 14000000 INFO @ Sun, 21 Jun 2020 17:45:47: 21000000 INFO @ Sun, 21 Jun 2020 17:45:47: 11000000 INFO @ Sun, 21 Jun 2020 17:45:50: 15000000 INFO @ Sun, 21 Jun 2020 17:45:52: 22000000 INFO @ Sun, 21 Jun 2020 17:45:53: 12000000 INFO @ Sun, 21 Jun 2020 17:45:56: 16000000 INFO @ Sun, 21 Jun 2020 17:45:58: 23000000 INFO @ Sun, 21 Jun 2020 17:45:58: 13000000 INFO @ Sun, 21 Jun 2020 17:46:02: 17000000 INFO @ Sun, 21 Jun 2020 17:46:02: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:46:02: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:46:02: #1 total tags in treatment: 23718285 INFO @ Sun, 21 Jun 2020 17:46:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:46:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:46:03: #1 tags after filtering in treatment: 23718284 INFO @ Sun, 21 Jun 2020 17:46:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:46:03: #1 finished! INFO @ Sun, 21 Jun 2020 17:46:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:46:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:46:04: 14000000 INFO @ Sun, 21 Jun 2020 17:46:05: #2 number of paired peaks: 321 WARNING @ Sun, 21 Jun 2020 17:46:05: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Sun, 21 Jun 2020 17:46:05: start model_add_line... INFO @ Sun, 21 Jun 2020 17:46:05: start X-correlation... INFO @ Sun, 21 Jun 2020 17:46:05: end of X-cor INFO @ Sun, 21 Jun 2020 17:46:05: #2 finished! INFO @ Sun, 21 Jun 2020 17:46:05: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 17:46:05: #2 alternative fragment length(s) may be 3,78 bps INFO @ Sun, 21 Jun 2020 17:46:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110790/SRX110790.05_model.r WARNING @ Sun, 21 Jun 2020 17:46:05: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:46:05: #2 You may need to consider one of the other alternative d(s): 3,78 WARNING @ Sun, 21 Jun 2020 17:46:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:46:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:46:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:46:09: 18000000 INFO @ Sun, 21 Jun 2020 17:46:10: 15000000 INFO @ Sun, 21 Jun 2020 17:46:15: 16000000 INFO @ Sun, 21 Jun 2020 17:46:15: 19000000 INFO @ Sun, 21 Jun 2020 17:46:21: 17000000 INFO @ Sun, 21 Jun 2020 17:46:22: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:46:27: 18000000 INFO @ Sun, 21 Jun 2020 17:46:29: 21000000 INFO @ Sun, 21 Jun 2020 17:46:32: 19000000 INFO @ Sun, 21 Jun 2020 17:46:36: 22000000 INFO @ Sun, 21 Jun 2020 17:46:38: 20000000 INFO @ Sun, 21 Jun 2020 17:46:42: 23000000 INFO @ Sun, 21 Jun 2020 17:46:44: 21000000 INFO @ Sun, 21 Jun 2020 17:46:47: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:46:47: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:46:47: #1 total tags in treatment: 23718285 INFO @ Sun, 21 Jun 2020 17:46:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:46:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:46:48: #1 tags after filtering in treatment: 23718284 INFO @ Sun, 21 Jun 2020 17:46:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:46:48: #1 finished! INFO @ Sun, 21 Jun 2020 17:46:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:46:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:46:49: #2 number of paired peaks: 321 WARNING @ Sun, 21 Jun 2020 17:46:49: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Sun, 21 Jun 2020 17:46:49: start model_add_line... INFO @ Sun, 21 Jun 2020 17:46:50: start X-correlation... INFO @ Sun, 21 Jun 2020 17:46:50: end of X-cor INFO @ Sun, 21 Jun 2020 17:46:50: #2 finished! INFO @ Sun, 21 Jun 2020 17:46:50: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 17:46:50: #2 alternative fragment length(s) may be 3,78 bps INFO @ Sun, 21 Jun 2020 17:46:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110790/SRX110790.10_model.r WARNING @ Sun, 21 Jun 2020 17:46:50: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:46:50: #2 You may need to consider one of the other alternative d(s): 3,78 WARNING @ Sun, 21 Jun 2020 17:46:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:46:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:46:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:46:50: 22000000 INFO @ Sun, 21 Jun 2020 17:46:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:46:55: 23000000 INFO @ Sun, 21 Jun 2020 17:46:59: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:46:59: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:46:59: #1 total tags in treatment: 23718285 INFO @ Sun, 21 Jun 2020 17:46:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:46:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:47:00: #1 tags after filtering in treatment: 23718284 INFO @ Sun, 21 Jun 2020 17:47:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:47:00: #1 finished! INFO @ Sun, 21 Jun 2020 17:47:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:47:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:47:01: #2 number of paired peaks: 321 WARNING @ Sun, 21 Jun 2020 17:47:01: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Sun, 21 Jun 2020 17:47:01: start model_add_line... INFO @ Sun, 21 Jun 2020 17:47:01: start X-correlation... INFO @ Sun, 21 Jun 2020 17:47:01: end of X-cor INFO @ Sun, 21 Jun 2020 17:47:01: #2 finished! INFO @ Sun, 21 Jun 2020 17:47:01: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 17:47:01: #2 alternative fragment length(s) may be 3,78 bps INFO @ Sun, 21 Jun 2020 17:47:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110790/SRX110790.20_model.r WARNING @ Sun, 21 Jun 2020 17:47:01: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:47:01: #2 You may need to consider one of the other alternative d(s): 3,78 WARNING @ Sun, 21 Jun 2020 17:47:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:47:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:47:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:47:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110790/SRX110790.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:47:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110790/SRX110790.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:47:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110790/SRX110790.05_summits.bed INFO @ Sun, 21 Jun 2020 17:47:16: Done! pass1 - making usageList (464 chroms): 2 millis pass2 - checking and writing primary data (11452 records, 4 fields): 27 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:47:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:47:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:48:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110790/SRX110790.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:48:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110790/SRX110790.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:48:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110790/SRX110790.10_summits.bed INFO @ Sun, 21 Jun 2020 17:48:02: Done! pass1 - making usageList (386 chroms): 1 millis pass2 - checking and writing primary data (5660 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:48:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110790/SRX110790.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:48:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110790/SRX110790.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:48:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110790/SRX110790.20_summits.bed INFO @ Sun, 21 Jun 2020 17:48:12: Done! pass1 - making usageList (148 chroms): 1 millis pass2 - checking and writing primary data (1050 records, 4 fields): 6 millis CompletedMACS2peakCalling